Gene sets UI, right sidebar refactor (#2097)

* prototyping

* render histos on open gene set

* prototyping

* render histos on open gene set

* factor out add genes to own component

* remove unused import

* mock reducer

* color by geneset stub

* menus and buttons

* geneset dialogue stub

* remove heatmap mock

* componetize histogram

* reenable add genes

* re-add isuserdefined

* test data

* remove have fetched

* add isExpanded state to gene, and pass to histogram

* expand button

* toggleable

* mini

* bump number of genes to 50

* don't clear diffexp on subset

* move create category to top

* render diffexp as geneset

* geneset show mean expression

* gene set reducer

* add geneset UI reducer

* wire e2e gene set loading prototype

* fix sniffing bug

* fix typo

* add gene modals

* client/src/actions/

* add autosave

* rename data-dir cli param

* add geneset, add gene, delete set

* prototype: remove csv upload placeholder

* handle delete gene from set

* prepopulate geneset with genes from modal

* add geneset: rename action

* icons, language consistency

* chevron after

* handle empty string case on genes for create geneset

* edit geneset

* fix language on create

* copy correction

* add popper2
upgrade react popper
upgrade react popper
adding popover2 package

* truncate uses tooltip2

* gene set button text typo

* remove logging

* moving server over

* remove test imports

* don't try to destructure map, use array.from

* fix add gene map datastructure error

* Revert "fix add gene map datastructure error"

This reverts commit b0eed45952.

* name --> genesetName, genes --> geneSymbols

* add gene to geneset, temporary format

* handle empty case, clear form input

* lint -- genesets wasn't passed via props

* userinfo

* move genes string to object conversion to action

* remove tmp gene description

* emptystring default for description

* remove empty string

* remove top level package json

* remove package lock as well

* remove flag for feature toggle

* remove comments in geneset

* comment cleanup

* remove comment

* revert diffexp genes to 10

* color by gene set

* disable color by gene set

* Gene menus are now inline, remove dead prototype code

* remove todo, magic number to variable

* remove jshint in rightsidebar

Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>

* remove unused geneset validation code

* tmp format pending geneset description

* move magic number into variable

* reorganize genesetsUI reducer pending tests

* rewire edit given new action name

* add basic validation and feedback for geneset name uniqueness

* mv annoDialog

* mv label, repair paths

* Update client/src/components/brushableHistogram/header.js

Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>

* add imports for icon in histo

* update jest snapshots given blueprint/tooltip2 usage of index -1

* ensure no empty paragraph

* intent from blueprint

* remove remainder of jshint references

* do not push undo when autosave fires

* fix autosave bugs

* remove todos

* clamp to util

* scient to util

* revert clearing diffexp

* rename value to be more specific stacked bar

* clean up logging and commetns

* remove gene entry tests pending rewrite

* tab index -1

* update jest snapshot, blueprint tooltip 2

* caret margin

* snapshot update

* ensure histogram is centered

* add geneset actions to config

* comment maybeScientific

* comment clamp

* comment ui reducer

* remove prototype code

* remove error log

* remove references to bl.ocks

* componetize parseBulkGeneString

* catch case where geneset rename same name

* genesetui reducer tests

* add geneset ui to index reducer config

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>

client/src/reducers/autosave.js

@@ -53,7 +53,7 @@ const Autosave = (
       return {
         ...state,
         genesetSaveInProgress: false,
-        lastSavedGenesets: nextSharedState.genesets,
+        lastSavedGenesets: nextSharedState.genesets.genesets,
       };
     }
 

client/src/reducers/config.js

@@ -1,4 +1,3 @@
-// jshint esversion: 6
 const Config = (
   state = {
     displayNames: null,

client/src/reducers/controls.js

@@ -1,5 +1,3 @@
-// jshint esversion: 6
-
 import _ from "lodash";
 import { subsetAndResetGeneLists } from "../util/stateManager/controlsHelpers";
 

client/src/reducers/differential.js

@@ -1,5 +1,3 @@
-// jshint esversion: 6
-
 const Differential = (
   state = {
     diffExp: null,

client/src/reducers/genesets.js

@@ -200,6 +200,7 @@ const GeneSets = (
      */
     case "geneset: add genes": {
       const { genesetName, genes } = action;
+
       if (!state.genesets.has(genesetName))
         throw new Error("geneset: add genes -- geneset name does not exist.");
 

client/src/reducers/genesetsUI.js

@@ -0,0 +1,88 @@
+/*
+Reducers for geneset UI-state.
+*/
+const GeneSetsUI = (
+  state = {
+    createGenesetModeActive: false,
+    isEditingGenesetName: false,
+    isAddingGenesToGeneset: false,
+  },
+  action
+) => {
+  switch (action.type) {
+    /**
+     * Activate interface for adding a new geneset
+     * No params, if the action is fired we flip
+     * a boolean here.
+     */
+    case "geneset: activate add new geneset mode": {
+      return {
+        ...state,
+        createGenesetModeActive: true,
+      };
+    }
+    /**
+     * Disable interface for adding a new geneset
+     * No params, if the action is fired we flip
+     * a boolean here.
+     */
+    case "geneset: disable create geneset mode": {
+      return {
+        ...state,
+        createGenesetModeActive: false,
+      };
+    }
+    /**
+     * Activate the interface for adding new genes to a geneset
+     * isAddingGenesToGeneset {
+     *  geneset: string, name of geneset
+     * },
+     */
+    case "geneset: activate add new genes mode": {
+      return {
+        ...state,
+        isAddingGenesToGeneset: action.geneset,
+      };
+    }
+    /**
+     * Disable the interface for adding new genes to a geneset
+     * No params, if the action is fired we flip
+     * a boolean here.
+     */
+    case "geneset: disable add new genes mode": {
+      return {
+        ...state,
+        isAddingGenesToGeneset: false,
+      };
+    }
+    /**
+     * Activate the interface for renaming a geneset
+     * isEditingGenesetName: {
+     *   type: "geneset: activate rename geneset mode",
+     *   data: geneset, // a string, name of geneset
+     * }
+     */
+    case "geneset: activate rename geneset mode": {
+      return {
+        ...state,
+        isEditingGenesetName: action.data,
+      };
+    }
+    /**
+     * Disable the interface for renaming a geneset
+     * No params, if the action is fired we flip
+     * a boolean here.
+     */
+    case "geneset: disable rename geneset mode": {
+      return {
+        ...state,
+        isEditingGenesetName: false,
+      };
+    }
+
+    default:
+      return state;
+  }
+};
+
+export default GeneSetsUI;

client/src/reducers/index.js

@@ -16,6 +16,7 @@ import layoutChoice from "./layoutChoice";
 import controls from "./controls";
 import annotations from "./annotations";
 import genesets from "./genesets";
+import genesetsUI from "./genesetsUI";
 import autosave from "./autosave";
 import ontology from "./ontology";
 import centroidLabels from "./centroidLabels";
@@ -33,6 +34,7 @@ const Reducer = undoable(
     ["ontology", ontology],
     ["annotations", annotations],
     ["genesets", genesets],
+    ["genesetsUI", genesetsUI],
     ["layoutChoice", layoutChoice],
     ["categoricalSelection", categoricalSelection],
     ["continuousSelection", continuousSelection],
@@ -58,6 +60,7 @@ const Reducer = undoable(
     "layoutChoice",
     "centroidLabels",
     "genesets",
+    "genesetsUI",
     "annotations",
   ],
   undoableConfig

client/src/reducers/undoableConfig.js

@@ -17,6 +17,8 @@ const skipOnActions = new Set([
   "window resize",
   "reset colorscale",
   "reset centroid labels",
+  "geneset: initial load",
+  "geneset: set tid",
 
   "graph brush change",
   "continuous metadata histogram brush",
@@ -30,6 +32,9 @@ const skipOnActions = new Set([
   "writable obs annotations - save complete",
   "writable obs annotations - save started",
   "writable obs annotations - save error",
+  "autosave: genesets started",
+  "autosave: genesets error",
+  "autosave: genesets complete",
 
   /* annotation component action */
   "annotation: activate add new label mode",
@@ -39,6 +44,14 @@ const skipOnActions = new Set([
   "annotation: activate edit label mode",
   "annotation: cancel edit label mode",
   "set annotations collection name",
+
+  /* geneset component action */
+  "geneset: activate add new geneset mode",
+  "geneset: disable create geneset mode",
+  "geneset: activate add new genes mode",
+  "geneset: disable add new genes mode",
+  "geneset: activate rename geneset mode",
+  "geneset: disable rename geneset mode",
 ]);
 
 /*
@@ -90,6 +103,14 @@ const saveOnActions = new Set([
   "annotation: label current cell selection",
   "annotation: delete label",
   "annotation: category edited",
+
+  /* geneset component action */
+  "geneset: create",
+  "geneset: delete",
+  "geneset: update",
+  "geneset: add genes",
+  "geneset: delete genes",
+  "geneset: set gene description",
 ]);
 
 /**